1. Department of Computer Science and Applied Mathematics,
2. Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
3. Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, 2153 Sheridan Road, Evanston, Illinois 60208, USA
4. Department of Biology, Carolina Center for Genome Sciences, and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
5. Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
6. Agilent Technologies Inc., Genomics—LSSU, 5301 Stevens Creek Boulevard, MS 3L/MT Santa Clara, California 95051, USA
7. Terrence Donnelly Centre for Cellular & Biomolecular Research,
8. Banting and Best Department of Medical Research, 160 College Street, Toronto, Ontario M5S 3E1, Canada
9. These authors contributed equally to this work.

Correspondence to: Jonathan Widom³Eran Segal^1,2 Correspondence and requests for materials should be addressed to J.W. (Email: j-widom@northwestern.edu) or E.S. (Email: eran.segal@weizmann.ac.il).

Abstract

Nucleosome organization is critical for gene regulation¹. In living cells this organization is determined by multiple factors, including the action of chromatin remodellers², competition with site-specific DNA-binding proteins³, and the DNA sequence preferences of the nucleosomes themselves^{4, 5, 6, 7, 8}. However, it has been difficult to estimate the relative importance of each of these mechanisms in vivo^{7, 9, 10, 11}, because in vivo nucleosome maps reflect the combined action of all influencing factors. Here we determine the importance of nucleosome DNA sequence preferences experimentally by measuring the genome-wide occupancy of nucleosomes assembled on purified yeast genomic DNA. The resulting map, in which nucleosome occupancy is governed only by the intrinsic sequence preferences of nucleosomes, is similar to in vivo nucleosome maps generated in three different growth conditions. In vitro, nucleosome depletion is evident at many transcription factor binding sites and around gene start and end sites, indicating that nucleosome depletion at these sites in vivo is partly encoded in the genome. We confirm these results with a micrococcal nuclease-independent experiment that measures the relative affinity of nucleosomes for 40,000 double-stranded 150-base-pair oligonucleotides. Using our in vitro data, we devise a computational model of nucleosome sequence preferences that is significantly correlated with in vivo nucleosome occupancy in Caenorhabditis elegans. Our results indicate that the intrinsic DNA sequence preferences of nucleosomes have a central role in determining the organization of nucleosomes in vivo.

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